[Biojava-l] SCF: support for ambiguities

[community at struck.lu]

Hello,


I am using the SCF class in the context of HIV-1 population sequencing. In
this context we do have sometimes ambiguous base calls. To support them I
extended the SCF class to allow for IUPAC ambiguities up to 2 nucleotides.

Therefore I simply added the following code to the "decode" function:

#########################
        public Symbol decode(byte call) throws IllegalSymbolException {

            //get the DNA Alphabet
            Alphabet dna = DNATools.getDNA();

            char c = (char) call;
            switch (c) {
                case 'a':
                case 'A':
                    return DNATools.a();
                case 'c':
                case 'C':
                    return DNATools.c();
                case 'g':
                case 'G':
                    return DNATools.g();
                case 't':
                case 'T':
                    return DNATools.t();
                case 'n':
                case 'N':
                    return DNATools.n();
                case '-':
                    return DNATools.getDNA().getGapSymbol();
                case 'w':
                case 'W':
                    //make the 'W' symbol
                    Set symbolsThatMakeW = new HashSet();
                    symbolsThatMakeW.add(DNATools.a());
                    symbolsThatMakeW.add(DNATools.t());
                    Symbol w = dna.getAmbiguity(symbolsThatMakeW);
                    return w;
                case 's':
                case 'S':
                    //make the 'S' symbol
                    Set symbolsThatMakeS = new HashSet();
                    symbolsThatMakeS.add(DNATools.c());
                    symbolsThatMakeS.add(DNATools.g());
                    Symbol s = dna.getAmbiguity(symbolsThatMakeS);
                    return s;
... (and so on)
#########################

Is this the right way to do it? And if so, how can this code be submitted to
the official biojava source code?


Best regards,
Daniel Struck
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